rs6815517

Positions:

• chr4-109808933-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.719 in 152,016 control chromosomes in the GnomAD database, including 39,523 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (39523 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.109808933C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109232 AN: 151898 Hom.: 39480 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.693

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.719 AC: 109328 AN: 152016 Hom.: 39523 Cov.: 31 AF XY: 0.720 AC XY: 53532 AN XY: 74304

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.696

Alfa AF: 0.703 Hom.: 6298

Bravo AF: 0.709

Asia WGS AF: 0.813 AC: 2826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6815517; hg19: chr4-110730089;